Thermal cycling is used to mimic the changes in oral cavity temperature experienced by composite resins when used clinically. The purpose of this study is to assess the thermal cycling effects of in-house produced composite resin on bonding strength. The dicalcium phosphate anhydrous filler surfaces are modified using nanocrystals and silanization (w/NP/Si). The resin is compared with commercially available composite resins Filtek Z250, Z350, and glass ionomer restorative material GIC Fuji-II LC (control). Different composite resins were filled into the dental enamel of bovine teeth. The bond force and resin–enamel junction graphical structures of the samples were determined after thermal cycling between 5 and 55 °C in deionized water for 600 cycles. After thermal cycling, the w/NP/Si 30 wt%, 50 wt% and Filtek Z250, Z350 groups showed higher shear forces than glass ionomer GIC, and w/NP/Si 50 wt% had the highest shear force. Through SEM observations, more of the fillings with w/NP/Si 30 wt% and w/NP/Si 50 wt% groups flowed into the enamel tubule, forming closed tubules with the composite resins. The push-out force is proportional to the resin flow depth and uniformity. The push-out tubule pore and resin shear pattern is the most uniform and consistent in the w/NP/Si 50 wt% group. Accordingly, this developed composite resin maintains great mechanical properties after thermal cycling. Thus, it has the potential to be used in a clinical setting when restoring non-carious cervical lesions.